WoS İndeksli Yayınlar Koleksiyonu / WoS Indexed Publications Collection

Permanent URI for this collectionhttps://hdl.handle.net/11147/7150

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  • Conference Object
  • Conference Object
    Reagent-Free Urea Determination From Hemodialysis Fluid: Development of FT-IR Spectroscopic Strategies
    (Springer, 2025) Akyuz, Ersed; Tanrisev, Mehmet; Guler, Gunnur
  • Article
    FW-S3PFCM: Feature-Weighted Safe-Semi Possibilistic Fuzzy C-Means Clustering
    (Springer, 2026) Khezri, Shirin; Aghazadeh, Nasser; Hashemzadeh, Mahdi; Golzari Oskouei, Amin
    The safe semi-supervised fuzzy c-means clustering (S3FCM) method is a well-known clustering method that can produce successful results by incorporating prior knowledge of the class distribution. Its process is fast and simple but still has two limitations. The first issue is that it gives equal weight to all data features, while in real-world applications, different features usually have different importance. Secondly, S3FCM is very sensitive to noise and outliers. This paper proposes an extension of the S3FCM, entitled FW-S3PFCM, to mitigate these shortcomings. The proposed method uses a local feature weighting scheme to consider the different feature weights in the clustering process. Additionally, a possibilistic version of the S3FCM is designed to reduce the sensitivity to noise and outliers. The effectiveness of the proposed method is comprehensively evaluated on various benchmark datasets, and its performance is compared with the state-of-the-arts methods. To practically asses the FW-S3FCM, a real-world dataset of brain MRI images and its segmentation performance are analyzed as well. The average Accuracy, F1-score, Sensitivity, and Precision measures obtained by FW-S3FCM are 0.9682, 0.9826, 0.9743, and 0.9925, respectively, which are better than the competitors' performance.
  • Article
    Alterations in Secondary Lipids Are Associated with Neuroinflammation in the Brain of Neu1-Deficient Mice
    (Springer, 2026) Ada, Ebru; Seyrantepe, Volkan
    Neu1 (lysosomal sialidase 1) is essential for removing sialic acid from oligosaccharides and glycoconjugates. Neu1 deficiency impairs lysosomal digestion, leading to sialidosis and sialoglycoprotein accumulation. It also increases lipids, including gangliosides GM3, GD3, GM4, and LM1, in the kidney, liver, and spleen. Neu1-/- mice display symptoms resembling Type II sialidosis, including enlarged spleen and liver, kidney issues, neurological problems, spinal defects, and oligosaccharide buildup. The study examined secondary lipid alterations and inflammation in the cortex and cerebellum of these mice. Lipidomic, molecular, and immunohistochemical analyses of tissues from 2 and 5 M Neu1-/- mice revealed reduced levels of lipids, including PC, PE, PS, and CL, along with increased pro-inflammatory cytokines and loss of oligodendrocytes and neurons. Signs of astrogliosis and microgliosis emerged in specific brain regions. These results indicate that reduced levels of glycerophospholipids could serve as an indicator of inflammation in sialidosis mice. Future research should investigate therapies targeting these lipid changes, as modulating glycerophospholipids might slow disease progression in sialidosis patients.
  • Article
    Application of 3D Cell Culture Techniques in Nanotoxicology: How Far Are We
    (Springer, 2026) Shakeri, Raheleh; Mirjalili, Seyedeh Zohreh; Karakus, Ceyda Oksel; Safavi, Maliheh
    Investigation of toxicological profile and possible side effects of engineered nanomaterials (ENMs) is of high importance. Historically, two-dimensional (2D) cell culture was used to study the toxicity of the ENMs, but due to their inability to simulate in vivo cell behavior, three-dimensional (3D) cell culture systems have been developed. Nanotoxicity studies initiate with in vitro experiments and continue with in vivo studies, which are very challenging and sometimes accompanied by conflicting data due to the in vitro-in vivo gap. Thus, scientists are turning their attention to microfabrication techniques and engineered systems "called organ-on-a-chips", which act as an intermediate between in vivo and in vitro systems. The present account tries to review the classical study models and suitably cover the emerging 3D culture models including scaffold-free and scaffold-based 3D cell cultures, 3D co-culture with direct contact and without cell-cell contact methods as well as microfluidic-based tissue chips and organoids. Overall, this review aims to give readers a better insight about the ENMs' toxicology and fill the gaps between the knowledge and practical techniques. Hopefully, the presented information will resolve the issues of 2D in vitro cultures and display the clinically relevant responses to the concerns of therapeutic ENMs.
  • Article
    Mn2+ Removal From Water Using a Strong Acidic Shallow Shell Resin: Performance and Response Surface Optimization
    (Springer, 2026) Gucur, G.; Recepoglu, Y. K.; Ozcan, D. O.; Arar, O.
    The removal of manganese ions (Mn2+) from aqueous solutions using a strong acid cation-exchange resin, Purolite SST60, was investigated in the present study. The influences of resin dosage, temperature, and pH on Mn2(+) removal were optimized using Response Surface Methodology based on a Central Composite Design. Results showed that removal efficiency was highly pH-dependent, increasing from 63% at pH 1.0 to over 99% at pH 3.0 and above. Even with only 0.01 g of resin, 98% removal was achieved, indicating high performance at low dosages. Equilibrium data aligned with the Langmuir isotherm, indicating monolayer sorption with a maximum capacity of 91.06 mg/g. Kinetic data followed a pseudo-second-order model. Thermodynamic analysis confirmed a spontaneous and exothermic process, supported by a negative enthalpy change and positive entropy change, likely due to dehydration of Mn2+ ions upon binding. Competitive ion studies revealed that divalent ions, particularly calcium and magnesium, significantly hinder Mn2+ removal, whereas monovalent ions had minimal impact. Complete desorption of Mn2+ was achieved using hydrochloric or nitric acid at concentrations of 0.5 mol/L and above, confirming the resin's reusability. Overall, Purolite SST60 offers an efficient, regenerable, and robust solution for manganese removal in water treatment applications.
  • Article
    Mass Spectrometric Profiling Reveals Alterations in N-Glycans and O-Glycans in Tay-Sachs Disease Under Autophagy-Induced Conditions
    (Springer, 2025) Can, Melike; Basirli, Hande; Jin, Chunsheng; Karlsson, Niclas G.; Bojar, Daniel; Seyrantepe, Volkan
    Tay-Sachs disease is a rare neurodegenerative disorder caused by mutations in the HEXA gene. The HEXA gene encodes the alpha-subunit of the enzyme beta-hexosaminidase A, which degrades GM2 ganglioside. Previously, we identified impaired autophagy in the brains of a mouse model of Tay-Sachs disease, which exhibited neuropathological and clinical abnormalities. Moreover, we demonstrated autophagosome clearance in Tay-Sachs cells under lithium-induced conditions. Here, we further aimed to evaluate N- and O-glycan changes in these cells and examine whether glycan alterations are linked to ER stress. The profiles of N- and O-glycans were analyzed using LC-MS/MS in fibroblasts and neuroglial cells from 5-month-old Hexa-/-Neu3-/- mice and neuroglial cells from Tay-Sachs patients under lithium induction and nutrient deprivation. The expression levels of ER stress-related markers were assessed using qRT-PCR and Western blot analyses. We demonstrated higher levels of high mannose and lower levels of complex types of N-glycans, along with increased O-glycan levels in Tay-Sachs cells. Compared to control groups, we observed upregulated expression of endoplasmic reticulum (ER) stress-related markers, CHOP and ATF-6, in Tay-Sachs cells. Our study demonstrated that autophagy induction causes the degradation of accumulated high-mannose N-glycans and O-glycans, which is associated with the downregulation of ER stress-related genes in Tay-Sachs cells. Our study is the first to show this phenomenon in Tay-Sachs cells and suggests the presence of ER stress-mediated autophagy. Therefore, targeting glycans through autophagy induction could offer therapeutic benefits to patients with Tay-Sachs disease in future studies.
  • Article
    Comparative Optimization of Hot Water and Citric Acid Extraction Methods for Sericin Recovery From Silk Cocoons: In Vitro Antioxidant and Antidiabetic Activities
    (Springer, 2026) Sincar, Bahar; Ozdemir, Feyza; Bicakci, Beyza Tutku; Erdem, Cansu; Yalcin, Dilek; Alamri, Abdulhakeem S.; Bayraktar, Oguz
    Silk sericin, a hydrophilic protein derived from Bombyx mori cocoons, has attracted increasing interest due to its antioxidant, moisturizing, and enzyme-inhibitory properties. Efficient extraction is essential to preserve its biofunctional potential. In this study, sericin was extracted using hot water and 1.25% (w/v) citric acid using autoclave-based heating to achieve pressurized conditions above 100 degrees C. A Box-Behnken Response Surface Methodology (RSM) was applied to systematically evaluate the effects of extraction parameters (temperature and time) and to optimize five key response variables: yield, purity, molecular weight and polydispersity index (PDI), total antioxidant capacity (ABTS), and alpha-glucosidase inhibition activity. The results revealed that higher temperatures (125 degrees C) produced the maximum sericin yield, while moderate conditions (115 degrees C for 45 min) ensured better preservation of antioxidant and antidiabetic activities. Hot acid extraction resulted in significantly enhanced purity and enzymatic inhibition compared to hot water extraction. Sericin fractions above 7 kDa exhibited the strongest bioactivity, as reflected by lower IC50 values in both ABTS and alpha-glucosidase inhibition assays. The optimized hot water citric acid-based method yielded 24.00% sericin with 100.00% purity and an IC50 of 0.67 mg/mL for alpha-glucosidase inhibition. This study compares hot water and hot acid autoclave extractions using Box-Behnken design and evaluates their effects on sericin yield, purity, and bioactivities. Citric acid-based extraction produced higher purity and stronger alpha-glucosidase inhibition, while hot water extraction preserved antioxidant potential more effectively. These findings support the use of citric acid as an eco-friendly and scalable extraction agent and highlight the potential of sericin in biomedical and nutraceutical applications.
  • Conference Object
    Applicability of Sound Criteria to Patients Undergoing Mastectomy
    (Springer, 2025) Ardila, Sara; Lupinacci, Kristin; Bayley, Erin; Cowher, Michael; Sabih, Quratulain; Steiman, Jennifer; Soran, Atilla
  • Article
    Citation - WoS: 8
    Protective and Therapeutic Effects of Milrinone on Acoustic Trauma in Rat Cochlea
    (Springer, 2019) Ceylan, Seyit Mehmet; Uysal, Erdal; Altinay, Serdar; Sezgin, Efe; Bilal, Nagihan; Petekkaya, Emine; Gulbagci, Mustafa Emre
    ObjectiveThe aim of this study was to investigate the potential protective and therapeutic effects of milrinone, a specific phosphodiesterase (PDE) III inhibitor, on acoustic trauma-induced cochlear injury and apoptosis.MethodsA total number of 30 healthy Wistar albino rats were evenly divided into five groups as follows: group 1 was assigned as control group; group 2 and 3 were assigned as low-dosage groups (0.25mg/kg) in which milrinone was administered 1h before acoustic trauma (AT) and 2h after AT, respectively; group 4 and 5 were assigned as high-dosage groups (0.50mg/kg) in which the drug was administered 1h before AT and 2h after AT, respectively. Except control group, all treatment groups received a single dosage of milrinone for 5days. Distortion product otoacoustic emissions (DPOAE) measurements were recorded before AT as well as at second and fifth post-traumatic days. At the end of fifth day, all rats were sacrificed and the cochlea of the rats was removed for histopathological evaluation. In addition, the groups were compared in terms of apoptotic index via caspase-3 staining.ResultsIn terms of signal-to-noise ratio (SNR), there was no statistically significant difference among the groups following AT (p>0.05). After 5days of milrinone treatment, the best SNR values were found in group 5, though all groups did not statistically differ (p>0.05). In histopathological evaluation, vacuolization, inflammation, and edema scores in all treatment groups were statistically lower than those of the control group (p<0.05). In group 2 and 4 where the drug was administered before AT, the inflammation and apoptosis index was lower than those of group 3 and 5 where the drug was administered after AT (p<0.0001).ConclusionWe reveal that milrinone has a protective effect on cochlear damage in the experimental acoustic model of rats. This protective effect was more apparent following the pre-traumatic milrinone administration, and is associated with its effect on decreasing inflammation and apoptosis. Based on DPOAE measurements following AT, especially in the group 5 (high-dosage group), milrinone may also have a therapeutic effect.